Starting phenix.real_space_refine on Wed Jul 1 22:30:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8jzr_36751/07_2026/8jzr_36751.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jzr_36751/07_2026/8jzr_36751.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jzr_36751/07_2026/8jzr_36751.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jzr_36751/07_2026/8jzr_36751.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8jzr_36751/07_2026/8jzr_36751.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8jzr_36751/07_2026/8jzr_36751.cif" model { file = "/net/cci-nas-00/data/ceres_data/8jzr_36751/07_2026/8jzr_36751.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jzr_36751/07_2026/8jzr_36751.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.060 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 2304 2.51 5 N 562 2.21 5 O 590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3474 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 3460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3460 Classifications: {'peptide': 456} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 437} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 0.90, per 1000 atoms: 0.26 Number of scatterers: 3474 At special positions: 0 Unit cell: (82.0652, 56.9432, 67.8294, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 18 16.00 O 590 8.00 N 562 7.00 C 2304 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 153 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG B 601 " - " ASN B 436 " Time building additional restraints: 0.26 Conformation dependent library (CDL) restraints added in 117.5 milliseconds 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 834 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 1 sheets defined 81.8% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'B' and resid 18 through 28 Processing helix chain 'B' and resid 34 through 57 removed outlier: 3.501A pdb=" N GLY B 38 " --> pdb=" O ARG B 34 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL B 40 " --> pdb=" O ALA B 36 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ASN B 57 " --> pdb=" O GLY B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 63 Processing helix chain 'B' and resid 70 through 98 removed outlier: 4.255A pdb=" N SER B 89 " --> pdb=" O THR B 85 " (cutoff:3.500A) Proline residue: B 90 - end of helix Processing helix chain 'B' and resid 101 through 118 Processing helix chain 'B' and resid 118 through 125 removed outlier: 3.866A pdb=" N LEU B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 134 removed outlier: 4.452A pdb=" N ALA B 130 " --> pdb=" O PRO B 126 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ALA B 131 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU B 132 " --> pdb=" O THR B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 184 removed outlier: 3.503A pdb=" N ASN B 174 " --> pdb=" O THR B 170 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR B 176 " --> pdb=" O LYS B 172 " (cutoff:3.500A) Proline residue: B 177 - end of helix removed outlier: 4.034A pdb=" N GLN B 182 " --> pdb=" O PHE B 178 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL B 183 " --> pdb=" O GLY B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 212 removed outlier: 3.989A pdb=" N ALA B 190 " --> pdb=" O ARG B 186 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N THR B 191 " --> pdb=" O GLY B 187 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG B 192 " --> pdb=" O PRO B 188 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN B 196 " --> pdb=" O ARG B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 220 removed outlier: 3.629A pdb=" N GLN B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 243 removed outlier: 3.503A pdb=" N ILE B 228 " --> pdb=" O THR B 224 " (cutoff:3.500A) Proline residue: B 229 - end of helix removed outlier: 3.849A pdb=" N PHE B 240 " --> pdb=" O ALA B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 327 Proline residue: B 323 - end of helix Processing helix chain 'B' and resid 328 through 348 removed outlier: 3.828A pdb=" N VAL B 343 " --> pdb=" O GLN B 339 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N HIS B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 389 removed outlier: 4.132A pdb=" N THR B 370 " --> pdb=" O ALA B 366 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE B 372 " --> pdb=" O TRP B 368 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASP B 373 " --> pdb=" O LEU B 369 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA B 374 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU B 379 " --> pdb=" O VAL B 375 " (cutoff:3.500A) Proline residue: B 382 - end of helix Processing helix chain 'B' and resid 390 through 395 removed outlier: 3.866A pdb=" N HIS B 395 " --> pdb=" O ILE B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 431 removed outlier: 3.953A pdb=" N LYS B 431 " --> pdb=" O LEU B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 479 removed outlier: 3.589A pdb=" N TYR B 458 " --> pdb=" O GLN B 454 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU B 460 " --> pdb=" O PRO B 456 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER B 469 " --> pdb=" O GLU B 465 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ILE B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 473 " --> pdb=" O SER B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 510 Processing helix chain 'B' and resid 531 through 558 removed outlier: 3.544A pdb=" N TYR B 535 " --> pdb=" O TYR B 531 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 349 through 350 removed outlier: 3.655A pdb=" N VAL B 442 " --> pdb=" O ILE B 439 " (cutoff:3.500A) 254 hydrogen bonds defined for protein. 759 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.39 Time building geometry restraints manager: 0.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 525 1.30 - 1.43: 963 1.43 - 1.55: 2041 1.55 - 1.68: 1 1.68 - 1.81: 27 Bond restraints: 3557 Sorted by residual: bond pdb=" CA ALA B 35 " pdb=" C ALA B 35 " ideal model delta sigma weight residual 1.524 1.439 0.085 1.32e-02 5.74e+03 4.17e+01 bond pdb=" CA ALA B 36 " pdb=" C ALA B 36 " ideal model delta sigma weight residual 1.523 1.451 0.072 1.30e-02 5.92e+03 3.09e+01 bond pdb=" C ALA B 36 " pdb=" O ALA B 36 " ideal model delta sigma weight residual 1.237 1.173 0.064 1.17e-02 7.31e+03 3.00e+01 bond pdb=" CA ALA B 31 " pdb=" C ALA B 31 " ideal model delta sigma weight residual 1.523 1.457 0.066 1.34e-02 5.57e+03 2.41e+01 bond pdb=" C CYS B 37 " pdb=" O CYS B 37 " ideal model delta sigma weight residual 1.236 1.186 0.050 1.16e-02 7.43e+03 1.89e+01 ... (remaining 3552 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 4684 1.92 - 3.84: 117 3.84 - 5.75: 28 5.75 - 7.67: 6 7.67 - 9.59: 2 Bond angle restraints: 4837 Sorted by residual: angle pdb=" C GLY B 28 " pdb=" N ALA B 29 " pdb=" CA ALA B 29 " ideal model delta sigma weight residual 121.86 131.24 -9.38 1.65e+00 3.67e-01 3.23e+01 angle pdb=" N ARG B 34 " pdb=" CA ARG B 34 " pdb=" C ARG B 34 " ideal model delta sigma weight residual 113.97 107.79 6.18 1.28e+00 6.10e-01 2.33e+01 angle pdb=" C ALA B 31 " pdb=" N GLY B 32 " pdb=" CA GLY B 32 " ideal model delta sigma weight residual 119.98 114.70 5.28 1.11e+00 8.12e-01 2.26e+01 angle pdb=" N PHE B 30 " pdb=" CA PHE B 30 " pdb=" C PHE B 30 " ideal model delta sigma weight residual 110.80 101.21 9.59 2.13e+00 2.20e-01 2.03e+01 angle pdb=" CA CYS B 37 " pdb=" C CYS B 37 " pdb=" N GLY B 38 " ideal model delta sigma weight residual 117.02 122.14 -5.12 1.17e+00 7.31e-01 1.91e+01 ... (remaining 4832 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.97: 1806 14.97 - 29.95: 184 29.95 - 44.92: 48 44.92 - 59.90: 6 59.90 - 74.87: 2 Dihedral angle restraints: 2046 sinusoidal: 745 harmonic: 1301 Sorted by residual: dihedral pdb=" CB CYS B 133 " pdb=" SG CYS B 133 " pdb=" SG CYS B 153 " pdb=" CB CYS B 153 " ideal model delta sinusoidal sigma weight residual 93.00 57.10 35.90 1 1.00e+01 1.00e-02 1.82e+01 dihedral pdb=" CA PRO B 390 " pdb=" C PRO B 390 " pdb=" N ILE B 391 " pdb=" CA ILE B 391 " ideal model delta harmonic sigma weight residual -180.00 -159.71 -20.29 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" N ARG B 33 " pdb=" C ARG B 33 " pdb=" CA ARG B 33 " pdb=" CB ARG B 33 " ideal model delta harmonic sigma weight residual 122.80 114.20 8.60 0 2.50e+00 1.60e-01 1.18e+01 ... (remaining 2043 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 506 0.065 - 0.130: 54 0.130 - 0.196: 7 0.196 - 0.261: 4 0.261 - 0.326: 1 Chirality restraints: 572 Sorted by residual: chirality pdb=" CA CYS B 37 " pdb=" N CYS B 37 " pdb=" C CYS B 37 " pdb=" CB CYS B 37 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CA ALA B 31 " pdb=" N ALA B 31 " pdb=" C ALA B 31 " pdb=" CB ALA B 31 " both_signs ideal model delta sigma weight residual False 2.48 2.24 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA PHE B 30 " pdb=" N PHE B 30 " pdb=" C PHE B 30 " pdb=" CB PHE B 30 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 569 not shown) Planarity restraints: 593 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 389 " -0.052 5.00e-02 4.00e+02 7.84e-02 9.82e+00 pdb=" N PRO B 390 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO B 390 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 390 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 28 " 0.013 2.00e-02 2.50e+03 2.55e-02 6.52e+00 pdb=" C GLY B 28 " -0.044 2.00e-02 2.50e+03 pdb=" O GLY B 28 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA B 29 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 187 " -0.037 5.00e-02 4.00e+02 5.70e-02 5.19e+00 pdb=" N PRO B 188 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 188 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 188 " -0.032 5.00e-02 4.00e+02 ... (remaining 590 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 1313 2.88 - 3.39: 3603 3.39 - 3.89: 5787 3.89 - 4.40: 6562 4.40 - 4.90: 11119 Nonbonded interactions: 28384 Sorted by model distance: nonbonded pdb=" O MET B 82 " pdb=" OG1 THR B 85 " model vdw 2.381 3.040 nonbonded pdb=" O GLN B 485 " pdb=" OG SER B 486 " model vdw 2.381 3.040 nonbonded pdb=" O ALA B 27 " pdb=" N ALA B 29 " model vdw 2.471 3.120 nonbonded pdb=" OD1 ASN B 436 " pdb=" ND1 HIS B 445 " model vdw 2.474 3.120 nonbonded pdb=" O ILE B 542 " pdb=" OG1 THR B 546 " model vdw 2.480 3.040 ... (remaining 28379 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 4.670 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 3559 Z= 0.456 Angle : 0.809 14.788 4842 Z= 0.467 Chirality : 0.048 0.326 572 Planarity : 0.006 0.078 592 Dihedral : 12.838 74.870 1209 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.45 % Allowed : 3.81 % Favored : 95.74 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.42), residues: 446 helix: 1.17 (0.29), residues: 344 sheet: None (None), residues: 0 loop : -1.76 (0.64), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 34 TYR 0.015 0.001 TYR B 335 PHE 0.020 0.001 PHE B 237 TRP 0.007 0.001 TRP B 452 HIS 0.001 0.000 HIS B 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00677 / 0.46 ( 3557) covalent geometry : angle 0.77243 / 0.46 ( 4837) SS BOND : bond 0.00260 / 0.14 ( 1) SS BOND : angle 0.40712 / 0.22 ( 2) hydrogen bonds : bond 0.16537 / 11.54 ( 254) hydrogen bonds : angle 6.49266 / 4.84 ( 759) link_NAG-ASN : bond 0.00362 / 0.19 ( 1) link_NAG-ASN : angle 9.69681 / 4.93 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.110 Fit side-chains REVERT: B 502 VAL cc_start: 0.8648 (p) cc_final: 0.8417 (t) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.0760 time to fit residues: 8.9390 Evaluate side-chains 67 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 454 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.158653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.133849 restraints weight = 4430.003| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.99 r_work: 0.3408 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3559 Z= 0.162 Angle : 0.609 6.152 4842 Z= 0.311 Chirality : 0.040 0.142 572 Planarity : 0.005 0.057 592 Dihedral : 4.119 16.976 483 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.36 % Favored : 96.41 % Rotamer: Outliers : 1.14 % Allowed : 13.07 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.42), residues: 446 helix: 1.69 (0.28), residues: 344 sheet: None (None), residues: 0 loop : -1.49 (0.68), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 33 TYR 0.014 0.001 TYR B 113 PHE 0.028 0.002 PHE B 240 TRP 0.011 0.001 TRP B 197 HIS 0.002 0.001 HIS B 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 ( 3557) covalent geometry : angle 0.60638 / 0.31 ( 4837) SS BOND : bond 0.00146 / 0.08 ( 1) SS BOND : angle 0.46050 / 0.25 ( 2) hydrogen bonds : bond 0.04583 / 3.23 ( 254) hydrogen bonds : angle 4.40706 / 3.27 ( 759) link_NAG-ASN : bond 0.00003 / 0.00 ( 1) link_NAG-ASN : angle 2.49650 / 1.25 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.110 Fit side-chains REVERT: B 57 ASN cc_start: 0.8004 (m-40) cc_final: 0.7778 (t0) REVERT: B 82 MET cc_start: 0.8179 (mmt) cc_final: 0.7963 (mmt) REVERT: B 196 ASN cc_start: 0.8458 (m-40) cc_final: 0.8196 (m-40) REVERT: B 320 LYS cc_start: 0.7838 (mttp) cc_final: 0.7486 (mttt) REVERT: B 326 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7873 (mp) REVERT: B 425 LYS cc_start: 0.6502 (ttmt) cc_final: 0.5761 (ttmt) REVERT: B 448 ASP cc_start: 0.8020 (t70) cc_final: 0.7539 (t0) REVERT: B 502 VAL cc_start: 0.8682 (p) cc_final: 0.8471 (t) outliers start: 4 outliers final: 2 residues processed: 71 average time/residue: 0.0492 time to fit residues: 4.5206 Evaluate side-chains 67 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 362 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 34 optimal weight: 0.1980 chunk 37 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 7 optimal weight: 0.3980 chunk 41 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 457 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.155500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.130326 restraints weight = 4311.739| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.96 r_work: 0.3362 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3559 Z= 0.155 Angle : 0.570 6.303 4842 Z= 0.291 Chirality : 0.038 0.145 572 Planarity : 0.004 0.053 592 Dihedral : 4.004 16.114 483 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.59 % Favored : 96.19 % Rotamer: Outliers : 3.12 % Allowed : 15.06 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.42), residues: 446 helix: 1.80 (0.28), residues: 351 sheet: None (None), residues: 0 loop : -1.60 (0.67), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 129 TYR 0.017 0.002 TYR B 113 PHE 0.022 0.002 PHE B 240 TRP 0.008 0.001 TRP B 197 HIS 0.002 0.001 HIS B 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 ( 3557) covalent geometry : angle 0.56835 / 0.29 ( 4837) SS BOND : bond 0.00437 / 0.23 ( 1) SS BOND : angle 0.65418 / 0.34 ( 2) hydrogen bonds : bond 0.04375 / 3.04 ( 254) hydrogen bonds : angle 4.25740 / 3.17 ( 759) link_NAG-ASN : bond 0.00003 / 0.00 ( 1) link_NAG-ASN : angle 1.95437 / 1.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.073 Fit side-chains REVERT: B 57 ASN cc_start: 0.8190 (m-40) cc_final: 0.7742 (t0) REVERT: B 82 MET cc_start: 0.8163 (mmt) cc_final: 0.7949 (mmt) REVERT: B 184 LYS cc_start: 0.8611 (ttpt) cc_final: 0.8373 (ttpt) REVERT: B 196 ASN cc_start: 0.8454 (m-40) cc_final: 0.8234 (m-40) REVERT: B 240 PHE cc_start: 0.8023 (OUTLIER) cc_final: 0.7533 (m-80) REVERT: B 326 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8078 (mp) REVERT: B 425 LYS cc_start: 0.6653 (ttmt) cc_final: 0.5896 (ttmt) REVERT: B 448 ASP cc_start: 0.7995 (t70) cc_final: 0.7478 (t0) outliers start: 11 outliers final: 6 residues processed: 76 average time/residue: 0.0623 time to fit residues: 5.7985 Evaluate side-chains 67 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 362 HIS Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 466 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 2 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 14 optimal weight: 0.0870 chunk 20 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.156894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.131974 restraints weight = 4286.229| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.94 r_work: 0.3380 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3559 Z= 0.125 Angle : 0.532 6.082 4842 Z= 0.271 Chirality : 0.037 0.137 572 Planarity : 0.004 0.039 592 Dihedral : 3.884 13.885 483 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.91 % Favored : 96.86 % Rotamer: Outliers : 2.56 % Allowed : 18.47 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.41), residues: 446 helix: 1.93 (0.28), residues: 355 sheet: None (None), residues: 0 loop : -2.12 (0.61), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 129 TYR 0.011 0.001 TYR B 113 PHE 0.016 0.001 PHE B 240 TRP 0.008 0.001 TRP B 197 HIS 0.001 0.000 HIS B 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 3557) covalent geometry : angle 0.53049 / 0.27 ( 4837) SS BOND : bond 0.00161 / 0.08 ( 1) SS BOND : angle 0.47884 / 0.25 ( 2) hydrogen bonds : bond 0.03958 / 2.77 ( 254) hydrogen bonds : angle 4.07616 / 3.04 ( 759) link_NAG-ASN : bond 0.00250 / 0.13 ( 1) link_NAG-ASN : angle 1.86364 / 1.06 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.070 Fit side-chains REVERT: B 82 MET cc_start: 0.8253 (mmt) cc_final: 0.8037 (mmt) REVERT: B 240 PHE cc_start: 0.7960 (OUTLIER) cc_final: 0.7461 (m-80) REVERT: B 326 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8075 (mp) REVERT: B 425 LYS cc_start: 0.6483 (ttmt) cc_final: 0.5952 (ttmt) REVERT: B 448 ASP cc_start: 0.8031 (t70) cc_final: 0.7485 (t0) REVERT: B 454 GLN cc_start: 0.8329 (tt0) cc_final: 0.7988 (mt0) outliers start: 9 outliers final: 6 residues processed: 66 average time/residue: 0.0497 time to fit residues: 4.2382 Evaluate side-chains 66 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 362 HIS Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 466 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 1 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 0.3980 chunk 27 optimal weight: 0.3980 chunk 40 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.155435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.130453 restraints weight = 4313.047| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.92 r_work: 0.3364 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3559 Z= 0.132 Angle : 0.534 6.070 4842 Z= 0.273 Chirality : 0.037 0.138 572 Planarity : 0.004 0.037 592 Dihedral : 3.880 13.853 483 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.69 % Allowed : 17.33 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.41), residues: 446 helix: 2.10 (0.28), residues: 350 sheet: None (None), residues: 0 loop : -1.72 (0.63), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 393 TYR 0.013 0.001 TYR B 113 PHE 0.018 0.001 PHE B 240 TRP 0.010 0.001 TRP B 197 HIS 0.001 0.000 HIS B 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 3557) covalent geometry : angle 0.53262 / 0.27 ( 4837) SS BOND : bond 0.00209 / 0.11 ( 1) SS BOND : angle 0.38658 / 0.20 ( 2) hydrogen bonds : bond 0.03955 / 2.78 ( 254) hydrogen bonds : angle 4.06380 / 3.02 ( 759) link_NAG-ASN : bond 0.00059 / 0.03 ( 1) link_NAG-ASN : angle 1.89549 / 1.10 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.116 Fit side-chains REVERT: B 151 ARG cc_start: 0.6013 (mpt180) cc_final: 0.5808 (mpt180) REVERT: B 240 PHE cc_start: 0.8029 (OUTLIER) cc_final: 0.7450 (m-80) REVERT: B 320 LYS cc_start: 0.8062 (mttp) cc_final: 0.7832 (mttm) REVERT: B 326 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8116 (mp) REVERT: B 393 ARG cc_start: 0.8111 (ttp80) cc_final: 0.7826 (ttm110) REVERT: B 425 LYS cc_start: 0.6531 (ttmt) cc_final: 0.5906 (ttmt) REVERT: B 448 ASP cc_start: 0.8018 (t70) cc_final: 0.7455 (t0) REVERT: B 454 GLN cc_start: 0.8403 (tt0) cc_final: 0.8134 (mt0) outliers start: 13 outliers final: 10 residues processed: 66 average time/residue: 0.0559 time to fit residues: 4.6618 Evaluate side-chains 70 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 362 HIS Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 466 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 0 optimal weight: 30.0000 chunk 16 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.155433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.129422 restraints weight = 4308.224| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.98 r_work: 0.3335 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3559 Z= 0.135 Angle : 0.537 6.213 4842 Z= 0.272 Chirality : 0.037 0.134 572 Planarity : 0.004 0.037 592 Dihedral : 3.886 13.843 483 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.41 % Allowed : 19.03 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.41), residues: 446 helix: 2.11 (0.28), residues: 352 sheet: None (None), residues: 0 loop : -1.76 (0.62), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 129 TYR 0.012 0.001 TYR B 113 PHE 0.018 0.001 PHE B 240 TRP 0.009 0.001 TRP B 197 HIS 0.001 0.000 HIS B 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 3557) covalent geometry : angle 0.53511 / 0.27 ( 4837) SS BOND : bond 0.00134 / 0.07 ( 1) SS BOND : angle 0.23605 / 0.13 ( 2) hydrogen bonds : bond 0.03946 / 2.78 ( 254) hydrogen bonds : angle 4.06809 / 3.02 ( 759) link_NAG-ASN : bond 0.00044 / 0.02 ( 1) link_NAG-ASN : angle 2.00955 / 1.18 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.117 Fit side-chains REVERT: B 151 ARG cc_start: 0.6036 (mpt180) cc_final: 0.5781 (mpt180) REVERT: B 240 PHE cc_start: 0.8082 (OUTLIER) cc_final: 0.7460 (m-80) REVERT: B 326 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8115 (mp) REVERT: B 425 LYS cc_start: 0.6463 (ttmt) cc_final: 0.5716 (ttmt) REVERT: B 448 ASP cc_start: 0.8058 (t70) cc_final: 0.7391 (t0) REVERT: B 454 GLN cc_start: 0.8410 (tt0) cc_final: 0.8179 (mt0) outliers start: 12 outliers final: 7 residues processed: 67 average time/residue: 0.0486 time to fit residues: 4.1703 Evaluate side-chains 65 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 362 HIS Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 442 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 40 optimal weight: 0.5980 chunk 1 optimal weight: 3.9990 chunk 15 optimal weight: 0.4980 chunk 24 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 0.0980 chunk 23 optimal weight: 0.7980 chunk 14 optimal weight: 0.0470 overall best weight: 0.3878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.157221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.131683 restraints weight = 4334.804| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.97 r_work: 0.3377 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3559 Z= 0.115 Angle : 0.514 5.905 4842 Z= 0.261 Chirality : 0.036 0.136 572 Planarity : 0.003 0.037 592 Dihedral : 3.816 13.150 483 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.84 % Allowed : 19.32 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.41), residues: 446 helix: 2.18 (0.28), residues: 352 sheet: None (None), residues: 0 loop : -1.75 (0.62), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 393 TYR 0.008 0.001 TYR B 113 PHE 0.016 0.001 PHE B 240 TRP 0.007 0.001 TRP B 197 HIS 0.001 0.000 HIS B 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 ( 3557) covalent geometry : angle 0.51281 / 0.26 ( 4837) SS BOND : bond 0.00050 / 0.03 ( 1) SS BOND : angle 0.22148 / 0.12 ( 2) hydrogen bonds : bond 0.03705 / 2.62 ( 254) hydrogen bonds : angle 4.04748 / 3.00 ( 759) link_NAG-ASN : bond 0.00148 / 0.08 ( 1) link_NAG-ASN : angle 1.61276 / 0.92 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.071 Fit side-chains REVERT: B 117 MET cc_start: 0.8644 (mmm) cc_final: 0.8439 (mmt) REVERT: B 151 ARG cc_start: 0.6011 (mpt180) cc_final: 0.5781 (mpt180) REVERT: B 240 PHE cc_start: 0.8017 (OUTLIER) cc_final: 0.7344 (m-80) REVERT: B 326 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8087 (mp) REVERT: B 425 LYS cc_start: 0.6442 (ttmt) cc_final: 0.5719 (ttmt) REVERT: B 448 ASP cc_start: 0.8038 (t70) cc_final: 0.7382 (t0) REVERT: B 454 GLN cc_start: 0.8339 (tt0) cc_final: 0.8120 (mt0) outliers start: 10 outliers final: 7 residues processed: 66 average time/residue: 0.0418 time to fit residues: 3.5136 Evaluate side-chains 66 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 362 HIS Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 466 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 15 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 5 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.152489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.126818 restraints weight = 4358.598| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.98 r_work: 0.3304 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3559 Z= 0.164 Angle : 0.567 6.179 4842 Z= 0.287 Chirality : 0.038 0.142 572 Planarity : 0.004 0.038 592 Dihedral : 3.924 14.210 483 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.12 % Allowed : 19.32 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.41), residues: 446 helix: 2.08 (0.28), residues: 352 sheet: None (None), residues: 0 loop : -1.84 (0.61), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 33 TYR 0.015 0.001 TYR B 113 PHE 0.022 0.001 PHE B 240 TRP 0.011 0.001 TRP B 197 HIS 0.002 0.000 HIS B 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.16 ( 3557) covalent geometry : angle 0.56605 / 0.29 ( 4837) SS BOND : bond 0.00016 / 0.01 ( 1) SS BOND : angle 0.17301 / 0.09 ( 2) hydrogen bonds : bond 0.04100 / 2.89 ( 254) hydrogen bonds : angle 4.15015 / 3.07 ( 759) link_NAG-ASN : bond 0.00215 / 0.11 ( 1) link_NAG-ASN : angle 1.46076 / 0.81 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.071 Fit side-chains REVERT: B 151 ARG cc_start: 0.6067 (mpt180) cc_final: 0.5778 (mpt180) REVERT: B 181 ASP cc_start: 0.8785 (m-30) cc_final: 0.8544 (m-30) REVERT: B 240 PHE cc_start: 0.8220 (OUTLIER) cc_final: 0.7509 (m-80) REVERT: B 326 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8164 (mp) REVERT: B 425 LYS cc_start: 0.6479 (ttmt) cc_final: 0.5924 (ttpt) REVERT: B 454 GLN cc_start: 0.8517 (tt0) cc_final: 0.8185 (mt0) outliers start: 11 outliers final: 8 residues processed: 61 average time/residue: 0.0504 time to fit residues: 3.8883 Evaluate side-chains 64 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 362 HIS Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 466 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 12 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 42 optimal weight: 0.5980 chunk 21 optimal weight: 0.0050 chunk 44 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.154774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.129466 restraints weight = 4305.066| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.95 r_work: 0.3352 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3559 Z= 0.126 Angle : 0.533 6.019 4842 Z= 0.271 Chirality : 0.037 0.135 572 Planarity : 0.003 0.037 592 Dihedral : 3.860 13.736 483 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.12 % Allowed : 19.03 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.41), residues: 446 helix: 2.13 (0.28), residues: 352 sheet: None (None), residues: 0 loop : -1.82 (0.61), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 129 TYR 0.010 0.001 TYR B 113 PHE 0.018 0.001 PHE B 240 TRP 0.007 0.001 TRP B 197 HIS 0.001 0.000 HIS B 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 3557) covalent geometry : angle 0.53169 / 0.27 ( 4837) SS BOND : bond 0.00041 / 0.02 ( 1) SS BOND : angle 0.19200 / 0.11 ( 2) hydrogen bonds : bond 0.03793 / 2.68 ( 254) hydrogen bonds : angle 4.10982 / 3.03 ( 759) link_NAG-ASN : bond 0.00154 / 0.08 ( 1) link_NAG-ASN : angle 1.43544 / 0.78 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.071 Fit side-chains REVERT: B 55 THR cc_start: 0.8054 (m) cc_final: 0.7829 (m) REVERT: B 151 ARG cc_start: 0.6076 (mpt180) cc_final: 0.5792 (mpt180) REVERT: B 240 PHE cc_start: 0.8109 (OUTLIER) cc_final: 0.7433 (m-80) REVERT: B 326 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8139 (mp) REVERT: B 425 LYS cc_start: 0.6443 (ttmt) cc_final: 0.5857 (ttpt) outliers start: 11 outliers final: 9 residues processed: 58 average time/residue: 0.0462 time to fit residues: 3.5024 Evaluate side-chains 62 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 362 HIS Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 466 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 44 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 38 optimal weight: 0.4980 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 42 optimal weight: 0.4980 chunk 13 optimal weight: 0.9990 chunk 18 optimal weight: 0.0670 chunk 6 optimal weight: 0.6980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 454 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.155732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.130065 restraints weight = 4314.270| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.98 r_work: 0.3355 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3559 Z= 0.120 Angle : 0.521 6.006 4842 Z= 0.264 Chirality : 0.037 0.135 572 Planarity : 0.003 0.036 592 Dihedral : 3.827 13.254 483 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.41 % Allowed : 18.75 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.41), residues: 446 helix: 2.15 (0.28), residues: 351 sheet: None (None), residues: 0 loop : -1.89 (0.60), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 129 TYR 0.009 0.001 TYR B 113 PHE 0.017 0.001 PHE B 240 TRP 0.007 0.001 TRP B 453 HIS 0.002 0.000 HIS B 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 3557) covalent geometry : angle 0.51999 / 0.26 ( 4837) SS BOND : bond 0.00059 / 0.03 ( 1) SS BOND : angle 0.19387 / 0.11 ( 2) hydrogen bonds : bond 0.03705 / 2.62 ( 254) hydrogen bonds : angle 4.05586 / 2.99 ( 759) link_NAG-ASN : bond 0.00131 / 0.07 ( 1) link_NAG-ASN : angle 1.39206 / 0.76 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.112 Fit side-chains REVERT: B 151 ARG cc_start: 0.6019 (mpt180) cc_final: 0.5754 (mpt180) REVERT: B 240 PHE cc_start: 0.8072 (OUTLIER) cc_final: 0.7379 (m-80) REVERT: B 326 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8140 (mp) REVERT: B 425 LYS cc_start: 0.6458 (ttmt) cc_final: 0.5860 (ttpt) outliers start: 12 outliers final: 8 residues processed: 60 average time/residue: 0.0477 time to fit residues: 3.8118 Evaluate side-chains 63 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 362 HIS Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 466 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 21 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.155613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.130158 restraints weight = 4319.474| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.98 r_work: 0.3358 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3559 Z= 0.124 Angle : 0.530 6.057 4842 Z= 0.268 Chirality : 0.037 0.133 572 Planarity : 0.003 0.036 592 Dihedral : 3.832 13.254 483 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.84 % Allowed : 19.32 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.42), residues: 446 helix: 2.16 (0.28), residues: 350 sheet: None (None), residues: 0 loop : -1.66 (0.63), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 129 TYR 0.010 0.001 TYR B 113 PHE 0.017 0.001 PHE B 240 TRP 0.008 0.001 TRP B 197 HIS 0.001 0.000 HIS B 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 3557) covalent geometry : angle 0.52881 / 0.27 ( 4837) SS BOND : bond 0.00055 / 0.03 ( 1) SS BOND : angle 0.20785 / 0.12 ( 2) hydrogen bonds : bond 0.03781 / 2.68 ( 254) hydrogen bonds : angle 4.07357 / 3.00 ( 759) link_NAG-ASN : bond 0.00141 / 0.07 ( 1) link_NAG-ASN : angle 1.32802 / 0.72 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 857.08 seconds wall clock time: 15 minutes 22.35 seconds (922.35 seconds total)